id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16547 Save X3D failure saving 2D labels ubaumann@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-14.7.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Trying to save as x3d Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex- > apo-overlay.2.cxs format session Log from Mon Dec 30 17:49:48 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex- > apo-overlay.2.cxs format session Log from Sun Dec 29 22:24:38 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/apo- > bound_PPEP3_1lettercode.transparencyup.2.cxs format session Log from Wed Dec 18 14:27:06 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/apo- > bound_PPEP3_1lettercode.cxs Log from Tue Dec 17 18:26:58 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/overlay-apo- > bound.cxs Log from Tue Dec 17 14:25:57 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay- > pepcomplex.4b.cxs"" Log from Sat Dec 14 13:28:52 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay- > pepcomplex.4b.cxs"" Log from Sat Dec 14 13:01:30 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay- > pepcomplex.4b.cxs"" Log from Sat Dec 14 12:48:22 2024UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.cxs"" Log from Sat Dec 14 00:29:48 2024 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show > open ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/nohd-WT-zn.cif"" Summary of feedback from opening /Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/nohd-WT-zn.cif --- warnings | Atom H11 has no neighbors to form bonds with according to residue template for BCN /B:702 Atom H12 has no neighbors to form bonds with according to residue template for BCN /B:702 notes | Fetching CCD BCN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/BCN/BCN.cif Fetching CCD PEG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif Chain information for nohd-WT-zn.cif #1 --- Chain | Description A | No description available B | No description available 50 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open /Users/ubaumann/Xtal/PPEP-geo/ESRF-20230721/Phenix- > wt_m1macbook/PPEP-4-3-XDSnewest/Refine_39/PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb Chain information for PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2 --- Chain | Description A | No description available B | No description available 50 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > hide #!1 models > show #!1 models > ui mousemode right pivot > ui mousemode right zoom > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!2 models > dssp #2 Computing secondary structure > dssp #2 minStrandLen 2 Computing secondary structure > dssp #2 minStrandLen 3 Computing secondary structure > dssp #2 minStrandLen 2 Computing secondary structure > ui mousemode right pivot > delete /B all Expected a keyword > delete /B attachedHyds Missing ""attachedHyds"" keyword's argument > delete /B ato Expected a keyword > delete /B atoms Expected a keyword > delete atoms /B > delete :HOH > hide atoms > show :ZN,153,154,157,190,196,197,111 atoms > hide :HOH > show /A:BCN atoms > delete elem H Missing or invalid ""atoms"" argument: invalid atoms specifier > delete atoms elem H Expected a keyword > delete atoms element H Expected a keyword > delete atoms H > color :21-150 & strand forestgreen ribbons > color :150-163 & helix darkorange ribbons > color :164-235 & helix cornflowerblue ribbons > color @C* slate gray atH Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color :21-149 & helix purple ribbons > color coil gray ribbons > color @C* slate gray atoms > set bgColor white > color coil silver ribbons > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-wt-3.cxs"" > color :164-235 & helix slateblue ribbons > style :153,154,157,190,196,197,111 ball Changed 140 atom styles > color :BCN@C* lightgrey > graphics silhouettes true > lighting shadows true > lighting shadows false > lighting full > lighting soft > lighting simple > lighting full > lighting shadows false > color :ZN pink > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-wt-3.cxs"" > hide :196 atoms > color :109-115 linnen ribb Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color :109-115 linen ribbons > color :109-115 light cyan ribbons > color 125:126 sea Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color :125,126 seagreen > color seagreen :125,126 ribb Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon-wt-3.cxs"" > label :153,154,157,190,197,111 text {0.name}{0.number} height 1.5 > label :153,154,157,190,197,111 text {0.name}{0.number} height 1. > ui mousemode right label > ui mousemode right ""move label"" > label :153,154,157,190,197,111 text {0.name}{0.number} height 1. > ui mousemode right ""move label"" > label :153,154,157,190,197,111 text ""text {0.residue.number}"" height 1. > label :153,154,157,190,197,111 text {0.residue.number} height 1. [Repeated 1 time(s)] > label :153,154,157,190,197,111 text {0.name}{0.number} height 1. > label :BCN text {0.name} height 1 > 2dlabels text edge > 2dlabels #3.1 xpos 0.493 ypos 0.618 > 2dlabels text S-loop > 2dlabels #3.2 xpos 0.757 ypos 0.771 > 2dlabels #3.1 xpos 0.494 ypos 0.624 > 2dlabels #3.2 xpos 0.760 ypos 0.730 > graphics silhouettes false > graphics silhouettes true > lighting full > lighting shadows false > lighting shadows true > 2dlabels text N > 2dlabels #3.3 xpos 0.076 ypos 0.895 > 2dlabels #3.1 xpos 0.503 ypos 0.626 > 2dlabels #3.1 xpos 0.502 ypos 0.637 > 2dlabels #3.2 xpos 0.748 ypos 0.715 > 2dlabels #3.3 xpos 0.068 ypos 0.913 > 2dlabels text C > 2dlabels #3.4 xpos 0.396 ypos 0.098 > 2dlabels #3.1 xpos 0.499 ypos 0.631 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt-shadows.png"" width 1567 height 1015 supersample 3 > view > ui tool show ""Side View"" > 2dlabels #3.3 xpos 0.069 ypos 0.946 > 2dlabels #3.4 xpos 0.425 ypos 0.124 > 2dlabels #3.1 xpos 0.514 ypos 0.678 > 2dlabels #3.3 xpos 0.051 ypos 0.910 > 2dlabels #3.4 xpos 0.411 ypos 0.067 > 2dlabels #3.1 xpos 0.501 ypos 0.638 > 2dlabels #3.1 xpos 0.498 ypos 0.635 > 2dlabels #3.4 xpos 0.410 ypos 0.096 > 2dlabels #3.3 xpos 0.053 ypos 0.906 > lighting shadows false > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon- > wt-3.labels.cxs"" > 2dlabels #3.2 xpos 0.737 ypos 0.725 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon- > wt-3.labels.cxs"" > show :161 atoms > hide :161 atoms > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon- > wt-3.labels.cxs"" > label :30 text β1 > label :30 text β1 height 1 > label :31 text β1 height 1 > label :31 text β1 height 1.2 > ui mousemode right label > label delete residues > label :31 text β1 height 1.3 > label delete residues > label :31 text β1 height 1.3 > ui mousemode right ""move label"" > label :53 text β2 height 1.3 > label :90 text β3 height 1.3 > label :133 text β4 height 1.3 > label :70 text 𝛼2 height 1.3 > label :77 text 𝛼3 height 1.3 > ui mousemode right label > label delete residues > label :31 text β1 height 1.3 [Repeated 1 time(s)] > ui mousemode right ""move label"" > label :53 text β2 height 1.3 > label :90 text β3 height 1.3 > label :133 text β4 height 1.3 > label :71 text 𝛼2 height 1.3 > label :81 text 𝛼3 height 1.3 > label :BCN text {0.name} height 1 > label :153,154,157,190,197,111 text {0.name}{0.number} height 1. > label :158 text 𝛼4 height 1.3 > label :200 text 𝛼7 height 1.3 > label :133 text β5 height 1.3 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon- > wt-3.labels-v2.cxs"" > 2dlabels #3.1 xpos 0.496 ypos 0.620 > label :125 text β4 height 1.3 > 2dlabels #3.1 xpos 0.502 ypos 0.624 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon- > wt-3.labels-v2.cxs"" > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt-shadows.png"" width 3134 height 2030 supersample 3 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon- > wt-3.labels-v3.cxs"" > label :178 text 𝛼5 height 1.3 > label :189 text 𝛼6 height 1.3 > label :226 text 𝛼9 height 1.3 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon- > wt-3.labels-v3.cxs"" > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt-shadows.png"" width 3134 height 2030 supersample 4 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/Ribbon- > wt-3.labels-v4.cxs"" > open /Users/ubaumann/Xtal/PPEP-geo/ESRF-20240430/FW30-4/Phenix- > FW30-4_M1Macbook/Refine_3/chain_A_E.pdb Chain information for chain_A_E.pdb #4 --- Chain | Description A | No description available E | No description available 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > mmaker #4 to #2 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb, chain A (#2) with chain_A_E.pdb, chain A (#4), sequence alignment score = 1080.2 RMSD between 177 pruned atom pairs is 0.531 angstroms; (across all 208 pairs: 1.506) > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.cxs"" > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/complex-to-wt.pdb"" > models #4 > hide #!2 models > hide #!3 models > dssp #4 minStrandLen 2 Computing secondary structure > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.cxs"" ——— End of log from Sat Dec 14 00:29:48 2024 ——— opened ChimeraX session > show #!2 models > hide #4 models > show #!3 models > 2dlabels #3.4 xpos 0.376 ypos 0.085 > 2dlabels #3.3 xpos 0.090 ypos 0.883 > 2dlabels #3.1 xpos 0.503 ypos 0.617 > 2dlabels #3.1 xpos 0.491 ypos 0.629 > 2dlabels #3.2 xpos 0.731 ypos 0.753 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.v2.cxs"" > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt.v2.png"" width 1567 height 1015 supersample 3 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt.v2.png"" width 3134 height 2030 supersample 3 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.v2.cxs"" > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt.v2.png"" width 1567 height 1015 supersample 3 > hide #!2 models > hide #!3 models > show #4 models > open ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/draw-complex_v2.cxc"" > dssp #4 minStrandLen 2 > hide atoms > show :ZN,153,154,157,190,197,111 atoms > show #4/E atoms > style #4/E ball Changed 110 atom styles > hide :HOH > show /A:BCN atoms > delete atoms H > color :21-149 & helix purple ribbons > color :21-150 & strand forestgreen ribbons > color :150-163 & helix darkorange ribbons > color :164-235 & helix slateblue ribbons > color #2:BCN@C* lightgrey > color :125,126 seagreen ribbons > color :ZN pink > color coil silver ribbons > color :109-115 light cyan ribbons > style :153,154,157,190,196,197,111 ball Changed 205 atom styles > label :153,154,157,190,197,111 text {0.name}{0.number} height 1. > label :BCN text {0.name} height 1 > label :31 text β1 height 1.3 > label :53 text β2 height 1.3 > label :90 text β3 height 1.3 > label :125 text β4 height 1.3 > label :133 text β5 height 1.3 > label :178 text 𝛼5 height 1.3 > label :189 text 𝛼6 height 1.3 > label :226 text 𝛼9 height 1.3 > label :200 text 𝛼7 height 1.3 > label #4:158 text 𝛼4 height 1.3 > color #4/A@C* slate gray atoms > color #4/E@C* cyan atoms executed draw-complex_v2.cxc > transparency 50 #4 rib Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency #4 50 ribbons > hide #!4 models > show #!2 models > ui mousemode right zoom > ui mousemode right ""move label"" > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.v3.cxs"" [Repeated 1 time(s)] > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt.v2.png"" width 1567 height 1015 supersample 3 > show #!3 models > 2dlabels #3.4 xpos 0.434 ypos 0.071 > 2dlabels #3.3 xpos 0.079 ypos 0.911 > 2dlabels #3.1 xpos 0.515 ypos 0.598 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt.v2.png"" width 1567 height 1015 supersample 3 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.v3.cxs"" > hide #!2 models > show #!4 models > 2dlabels #3.2 xpos 0.790 ypos 0.625 > 2dlabels #3.4 xpos 0.361 ypos 0.078 > 2dlabels #3.3 xpos 0.300 ypos 0.767 > 2dlabels #3.2 xpos 0.773 ypos 0.617 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/complex.png"" > width 3134 height 2030 supersample 3 > 2dlabels #3.1 xpos 0.515 ypos 0.598 > 2dlabels #3.1 xpos 0.516 ypos 0.590 > ui mousemode right zoom > ui mousemode right ""move label"" > 2dlabels #3.4 xpos 0.338 ypos 0.125 > 2dlabels #3.3 xpos 0.284 ypos 0.849 > hide #!4 models > show #!2 models > 2dlabels #3.4 xpos 0.405 ypos 0.122 > 2dlabels #3.4 xpos 0.437 ypos 0.077 > 2dlabels #3.3 xpos 0.074 ypos 0.960 > 2dlabels #3.1 xpos 0.543 ypos 0.612 > 2dlabels #3.1 xpos 0.543 ypos 0.621 > show #!4 models > hide #!4 models > show #!4 models > hide #!2 models > show #!2 models > hide #!4 models > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt.v3.png"" width 3412 height 2334 supersample 4 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.v4.cxs"" > hide #!2 models > show #!4 models > 2dlabels #3.3 xpos 0.312 ypos 0.804 > 2dlabels #3.4 xpos 0.366 ypos 0.079 > style #4/E stick Changed 56 atom styles > 2dlabels #3.1 xpos 0.541 ypos 0.611 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > label #4:158 text 𝛼4 height 1.3 > hide #!4 models > show #!4 models > show #!2 models > hide #!2 models > select add #2 1777 atoms, 1822 bonds, 6 pseudobonds, 219 residues, 3 models selected > select subtract #2 Nothing selected > show #!2 models > hide #!2 models > label #4:81 text 𝛼3 height 1.33 > label #4:68 text 𝛼2 height 1.3 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.v4.cxs"" > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-complex.v3.png"" width 1706 height 1167 supersample 3 > style #4 sticks Expected a keyword > style #4 sticks at Expected a keyword > style #4 at stick Expected a keyword > style #4 stick Changed 1747 atom styles > style #4:ZN ball Changed 1 atom style > style #4:ZN sphere Changed 1 atom style > hide #!4 models > show #!2 models > 2dlabels #3.3 xpos 0.075 ypos 0.968 > 2dlabels #3.4 xpos 0.438 ypos 0.074 > 2dlabels #3.1 xpos 0.543 ypos 0.618 > label #2:217 text 𝛼8 height 1.3 > 2dlabels #3.2 xpos 0.799 ypos 0.652 > show :113 atoms > style :113 sticks Expected a keyword > style :113 ball Changed 36 atom styles > label :113 text {0.name}{0.number} height 1. > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-wt.v3.png"" width 1706 height 1167 supersample 4 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.v4.cxs"" > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!2 models > show #!4 models > style #4:113 stick Changed 12 atom styles > 2dlabels #3.4 xpos 0.371 ypos 0.082 > 2dlabels #3.3 xpos 0.314 ypos 0.808 > 2dlabels #3.1 xpos 0.543 ypos 0.607 > 2dlabels #3.2 xpos 0.784 ypos 0.580 > select #4/A:113@OH 1 atom, 1 residue, 1 model selected > select add #4/E:5@O 2 atoms, 2 residues, 1 model selected > distance #4/A:113@OH #4/E:5@O Distance between chain_A_E.pdb #4/A TYR 113 OH and /E PRO 5 O: 2.717Å > ~distance > select clear > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay-pepcomplex- > wt.v4.bcxs.cxs"" > open ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/n-pseudobonds.pb"" Line 4 ""/a:701@ZN /a:197@oe1 "", got 2 atoms for spec ""/a:701@ZN"", require exactly 1 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay- > pepcomplex.4b.cxs"" ——— End of log from Sat Dec 14 12:48:22 2024 ——— opened ChimeraX session > open ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/n-pseudobonds.pb"" Opened Pseudobonds n-pseudobonds.pb, 5 bonds > show #4/a:196 atoms > show /a:196 atoms > show #!2 models > hide #!2 models > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay- > pepcomplex.4b.cxs"" > label #4/a:157 text {0.name}{0.number} height 0.8 > 2dlabels #3.4 xpos 0.362 ypos 0.082 > 2dlabels #3.3 xpos 0.313 ypos 0.812 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay- > pepcomplex.4b.cxs"" > open ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/n-pseudobonds.pb"" Opened Pseudobonds n-pseudobonds.pb, 7 bonds > label #4/a:196 text {0.name}{0.number} height 1.3 > label #4/a:196 text {0.name}{0.number} height 1. > label #4/a:196 text {0.name}{0.number} height 0.9 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay- > pepcomplex.4b.cxs"" ——— End of log from Sat Dec 14 13:01:30 2024 ——— opened ChimeraX session > transparency #4 0 cartoons > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-complex.v4.notransp.png"" width 3412 height 2334 supersample 3 > label #2/a:47 text 𝛼1 height 1.3 > show #!2 models > hide #!2 models > label #4/a:47 text 𝛼1 height 1.3 > transparency #4 60 cartoons > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-complex.v4.png"" width 3412 height 2334 supersample 3 > 2dlabels ""P1"" Expected 'all' or a 2d label name or a label models specifier or a keyword > 2dlabels text P1 > 2dlabels #3.5 xpos 0.500 ypos 0.500 > ~2dlabels text ""P1"" > 2dlabels delete text ""P1"" Expected 'all' or a label/arrow models specifier or a keyword > ~2dlabels ""P1"" > 2dlabels delete ""P1"" Expected 'all' or a label/arrow models specifier or a keyword > 2dlabels #3.5 xpos 0.655 ypos 0.525 > ~2dlabels ""P11"" color cyan > 2dlabels delete ""P11"" color cyan Expected 'all' or a label/arrow models specifier or a keyword > ~2dlabels text ""P1"" color cyan > 2dlabels delete text ""P1"" color cyan Expected 'all' or a label/arrow models specifier or a keyword > 2dlabels text P1 color cyan > 2dlabels #3.6 xpos 0.675 ypos 0.511 [Repeated 1 time(s)] > ~2dlabels #3.6 > ~2dlabels #3.5 > 2dlabels text P1 color cyan > 2dlabels #3.5 xpos 0.656 ypos 0.520 > 2dlabels text P1' color cyan > 2dlabels #3.6 xpos 0.638 ypos 0.605 > 2dlabels #3.5 xpos 0.651 ypos 0.521 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/PNGs/cartoon- > ppep-3-complex.v4b.png"" width 3412 height 2334 supersample 4 > label #4/a:153 text {0.name}{0.number} height 0.9 > label #4/a:153 text {0.name}{0.number} height 0.8 > 2dlabels #3.2 xpos 0.776 ypos 0.578 > save ""/Users/ubaumann/Sync/PPEP-Geo Manuscript/Figures/oerlay- > pepcomplex.4b.cxs"" ——— End of log from Sat Dec 14 13:28:52 2024 ——— opened ChimeraX session > 2dlabels #3.1 xpos 0.553 ypos 0.608 > 2dlabels #3.3 xpos 0.336 ypos 0.825 > 2dlabels #3.4 xpos 0.354 ypos 0.079 > 2dlabels #3.3 xpos 0.319 ypos 0.828 > 2dlabels #3.6 xpos 0.637 ypos 0.614 > 2dlabels #3.5 xpos 0.657 ypos 0.602 > 2dlabels #3.6 xpos 0.632 ypos 0.624 > 2dlabels #3.5 xpos 0.658 ypos 0.603 > 2dlabels #3.6 xpos 0.630 ypos 0.626 > label #4/A:111 text {0.name} size 25 height fixed > label #4/A:111 text {0.name} {0.number}size 25 height fixed Expected a keyword > label #4/A:111 text {0.name} {0.number} size 25 height fixed Expected a keyword > label #4/A:111 text ""{0.name} {0.number}"" size 25 height fixed > label #4/A:111 text ""{0.name} {0.number}"" size 20 height fixed > 2dlabels #3.2 text S-loop color light cyan size 25 > 2dlabels #3.2 text S-loop color lsky size 25 Invalid ""color"" argument: Expected one of 'auto' or 'default' or a color > 2dlabels #3.2 text S-loop color skyblue size 25 > 2dlabels #3.2 xpos 0.787 ypos 0.570 > 2dlabels #3.5 text P1 color cyan bold true size 25 > 2dlabels #3.6 text P1' color cyan bold true size 25 > 2dlabels #3.6 text P2' color cyan bold true size 25 > 2dlabels #3.6 text P1' color cyan bold true size 25 > 2dlabels ext ""P2'"" color cyan bold true size 25 Expected 'all' or a 2d label name or a label models specifier or a keyword > 2dlabels text P2' color cyan bold true size 25 > 2dlabels #3.7 xpos 0.681 ypos 0.516 > 2dlabels text P2 color cyan bold true size 25 > 2dlabels #3.8 xpos 0.654 ypos 0.445 > 2dlabels text P3 color cyan bold true size 25 > 2dlabels #3.9 xpos 0.594 ypos 0.583 > 2dlabels #3.6 xpos 0.635 ypos 0.623 > 2dlabels #3.5 xpos 0.651 ypos 0.523 > 2dlabels #3.7 xpos 0.683 ypos 0.522 > 2dlabels #3.5 xpos 0.654 ypos 0.598 > 2dlabels #3.4 xpos 0.356 ypos 0.083 > 2dlabels #3.3 xpos 0.323 ypos 0.830 > 2dlabels #3.3 text N true size 30 Expected a keyword > 2dlabels #3.3 text N size 30 > 2dlabels #3.4 text C size 35 > 2dlabels #3.3 text N size 35 > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/peptidecomplex.cxs > transparency #4 40 ribbons > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/Pepcomplex_1.png > width 2632 height 1802 supersample 3 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #2 atoms > ~label #2 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #2/A:111,190,113 atoms > style #2 stick Changed 1777 atom styles > transparence #2 60 at Unknown command: transparence #2 60 at > transparency #2 60 atoms > transparency #2 80 atoms > transparency #2 60 ribbons > transparency #2 80 ribbons > transparency #4 20 ribbons > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/overlay-apo- > bound.cxs ——— End of log from Tue Dec 17 14:25:57 2024 ——— opened ChimeraX session > show #2/B:191 atoms > show #2/A:191 atoms > show #4/A:191 atoms > ui mousemode right ""move label"" > 2dlabels #3.2 xpos 0.848 ypos 0.655 > label #4/A:190,113,196,197,111,190,191,153,157 text{0.1}{0.number} size 20 > height fix Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label #4/A:190,113,196,197,111,190,191,153,157 text {0.1}{0.number} size 20 > height fixed > label #4/A:190,113,196,197,111,190,191,153,157 text {0.1-letter}{0.number} > size 20 height fixed > label #4/A:190,113,196,197,111,190,191,153,157 text {0.code}{0.number} size > 20 height fixed > label #4/A:190,113,196,197,111,190,191,153,157 code,number size 20 height > fix Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label #4/A:190,113,196,197,111,190,191,153,157 ""code,number"" size 20 height > fix Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label #4/A:190,113,196,197,111,190,191,153,157 attribute code,number size 20 > height fixed > label #4/A:190,113,196,197,111,190,191,153,157 text ""{0.1-letter > code}{0.number}"" size 20 height fixed > label #4/A:154,190,113,196,197,111,190,191,153,157 text ""{0.1-letter > code}{0.number}"" size 20 height fixed > label #4/A:154,190,113,196,197,111,190,191,153,157 text ""{0.1-letter > code}{0.number}"" size 25 height fixed > show#2/A:154 at Unknown command: show#2/A:154 at > show #2/A:154 atoms > label #4/A:154,190,113,196,197,111,190,191,153,157 text ""{0.1-letter > code}{0.number}"" size 25 height fixed > label #4/A:154,190,113,196,197,111,190,191,153,157 text {0.code}{0.number} > size 25 height fixed > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > label #4/A:154,190,113,196,197,111,190,191,153,157 text {0.number} size 25 > height fixed > select #4/A:154,190,113,196,197,111,190,191,153,157 88 atoms, 87 bonds, 2 pseudobonds, 9 residues, 2 models selected > label (#!4 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > select #4/A::190 text ""Y/F 190"" size 20 height fix Expected an objects specifier or a keyword > label #4/A::190 text ""Y/F 190"" size 20 height fix Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label #4/A:190 text ""Y/F 190"" size 20 height fixed > select clear > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/overlay-apo- > bound.2.png width 1816 height 1243 supersample 3 > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/apo- > bound_PPEP3_1lettercode.cxs ——— End of log from Tue Dec 17 18:26:58 2024 ——— opened ChimeraX session > label #4/A:154 text ""E/A 154"" size 20 height fixed > ui mousemode right ""move label"" > 2dlabels #3.3 xpos 0.003 ypos 0.951 > 2dlabels #3.4 xpos 0.334 ypos 0.072 > 2dlabels #3.5 xpos 0.679 ypos 0.591 > 2dlabels #3.6 xpos 0.644 ypos 0.614 > 2dlabels #3.7 xpos 0.718 ypos 0.515 > 2dlabels #3.9 xpos 0.619 ypos 0.597 > 2dlabels #3.6 xpos 0.657 ypos 0.618 > 2dlabels #3.9 xpos 0.619 ypos 0.571 > 2dlabels #3.8 xpos 0.682 ypos 0.445 [Repeated 1 time(s)] > 2dlabels #3.9 xpos 0.619 ypos 0.575 > 2dlabels #3.6 xpos 0.654 ypos 0.622 > 2dlabels #3.2 xpos 0.931 ypos 0.661 > select ~sel & ##selected Nothing selected > lable #4/A:153,157196,197,113,111,191 text ""{0.label_1_letter_code}{0.name}"" > size 25 height fixed Unknown command: lable #4/A:153,157196,197,113,111,191 text ""{0.label_1_letter_code}{0.name}"" size 25 height fixed > label #4/A:153,157196,197,113,111,191 text {0.label_1_letter_code}{0.name} > size 25 height fixed > select #4/A:113@CG 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > label sel attribute label_one_letter_code > label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > label #4/A:153,157196,197,113,111,191 text {0.label_one_letter_code}{0.name} > size 25 height fixed > label #4/A:153,157196,197,113,111,191 text {0.label_one_letter_code}{0.name} > size 20 height fixed > ~label > label #4/A:153,157196,197,113,111,191 text {0.label_one_letter_code}{0.name} > size 20 height fixed > ~label > select clear > label #4/A:153,157196,197,113,111,191 text {0.label_one_letter_code}{0.name} > size 20 height fixed > label #4/A:153,157196,197,113,111,191 text > {0.label_one_letter_code}{0.number} size 20 height fixed > label #4/A:153,157,196,197,113,111,191 text > {0.label_one_letter_code}{0.number} size 20 height fixed > label #4/A:154 text ""E/A 154"" size 20 height fixed > label #4/A:190 text ""Y/F 190"" size 20 height fixed > 2dlabels #3.3 xpos -0.001 ypos 0.958 > 2dlabels #3.4 xpos 0.335 ypos 0.073 > label #4/A:104 text η4 height fixed size 30 > transparency #2 90 > transparency #2 95 > ribbon > transparency #2 95 ribbons > transparency #2 90 ribbons > transparency #2 93 ribbons > 2dlabels #3.1 xpos 0.552 ypos 0.612 > 2dlabels #3.5 xpos 0.682 ypos 0.517 > 2dlabels #3.6 xpos 0.667 ypos 0.608 > 2dlabels #3.7 xpos 0.719 ypos 0.516 > hide #4/E ribbons > transparency #2 91 ribbons > color #4 grey coil Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #4 grey ribbons & coil Expected ',' or a keyword > color #4 & coil grey ribbons > color #4 & coil lightgrey ribbons > color #4 & coil silver ribbons > 2dlabels #3.6 xpos 0.672 ypos 0.601 > label #4/A:192 text 𝛼6 height fixed size 30 > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/overlay-apo- > bound.4.png width 1281 height 1077 supersample 3 > hide #4/A:111 atoms > show #4/A:111 atoms > transparency 70 #4/A:111 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 70 #4/A:111 at Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency #4/A:111 70 atoms > transparency #4/A:111 60 atoms > transparency #4/A:111 50 atoms > transparency #4/A:111 40 atoms > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/overlay-apo- > bound.4.png width 1562 height 1313 supersample 3 > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/apo- > bound_PPEP3_1lettercode.transparencyup.2.cxs ——— End of log from Wed Dec 18 14:27:06 2024 ——— opened ChimeraX session > transparency #4/A 0 cartoons,atoms > transparency #42A 95 cart,at Missing or invalid ""percent"" argument: Expected a number > transparency #2A 95 cart,at Missing or invalid ""percent"" argument: Expected a number > transparency #2/A 95 cartoons,atoms > 2dlabels #3.8 xpos 0.679 ypos 0.449 > transparency #2/A 90 cartoons,atoms > 2dlabels #3.7 xpos 0.717 ypos 0.517 > label #4/E:7 text P3' height fixed size 25 color cyan > 2dlabels #3.3 xpos 0.001 ypos 0.947 > 2dlabels #3.4 xpos 0.330 ypos 0.096 > 2dlabels #3.1 xpos 0.563 ypos 0.610 > 2dlabels #3.2 xpos 0.936 ypos 0.655 > 2dlabels #3.4 xpos 0.348 ypos 0.102 > 2dlabels #3.3 xpos 0.010 ypos 0.950 > 2dlabels #3.1 xpos 0.574 ypos 0.613 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex- > apo-overlay.2.cxs ——— End of log from Sun Dec 29 22:24:38 2024 ——— opened ChimeraX session > show #2,4/A:101 atoms > distance #2/A:113@CA #4/A:113@CA color hotpink dig 1 Expected a keyword > distance #2/A:113@CA #4/A:113@CA color hotpink decimalPlaces 1 Distance between PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A TYR 113 CA and chain_A_E.pdb #4/A TYR 113 CA: 3.8Å > 2dlabels #3.3 xpos 0.285 ypos 0.808 > distance #2/A:101@CA #4/A:101@CA color hotpink decimalPlaces 1 Distance between PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ILE 101 CA and chain_A_E.pdb #4/A ILE 101 CA: 2.7Å > distance #2/A:101@CA #4/A:101@CA color cyan decimalPlaces 1 Distance already exists; modify distance properties with 'distance style' > distance style color cyan decimalPlaces 1 > distance style color cyan > distance style color hotpink decimalPlaces 1 > distance style color hotpink > distance #2/A:191@CG #4/A:191@CG color hotpink decimalPlaces 1 Distance between PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A PHE 191 CG and chain_A_E.pdb #4/A PHE 191 CG: 1.8Å > close #3.5-9 > label #4/E:6 text P2' size 25 color navy > label #4/E:6 text P2' size 25 height fixed color blue > label #4/E:6 text P2' size 25 height fixed color cyan > label #4/E:5 text P1' size 25 height fixed color cyan > label #4/E:4 text P1 size 25 height fixed color cyan > label #4/E:3 text P2 size 25 height fixed color cyan > label #4/E:2 text P3 size 25 height fixed color cyan > distance #2/A:111@CG #4/A:111@CG color hotpink decimalPlaces 1 Distance between PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ARG 111 CG and chain_A_E.pdb #4/A ARG 111 CG: 5.2Å > label #4/A:101 text {0.one_letter_code}{0.number} height fixed size 25 > select #4/E:3 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel color #fa4743 interModel false intraRes false reveal true 2 hydrogen bonds found > select clear > 2dlabels #3.3 xpos 0.292 ypos 0.810 > label #4/A:103 text η3 height fixed size 30 > label #4/A:103 text η3 height fixed size 30 color white > label #4/A:104 text η4 height fixed size 30 color white > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex- > apo-overlay.2.cxs > label #4/E:2 text P3 size 25 height fixed color blue > label #4/E:3 text P2 size 25 height fixed color blue > label #4/E:4 text P1 size 25 height fixed color blue > label #4/E:5 text P1' size 25 height fixed color blue > label #4/E:6 text P2' size 25 height fixed color blue > label #4/E:7 text P3' size 25 height fixed color blue > ~distance #4/A:101@CG #2/A:101@CG > ~distance #4/A:111@CG #2/A:111@CG > distance #4/A:111@CA #2/A:111@CA color hotpink decimalPlaces 1 Distance between chain_A_E.pdb #4/A ARG 111 CA and PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ARG 111 CA: 3.9Å > 2dlabels #3.4 xpos 0.277 ypos 0.033 > 2dlabels #3.3 xpos 0.209 ypos 0.858 > 2dlabels #3.1 xpos 0.533 ypos 0.627 > 2dlabels #3.2 xpos 0.933 ypos 0.683 > 2dlabels #3.4 xpos 0.296 ypos 0.065 > 2dlabels #3.3 xpos 0.225 ypos 0.825 > 2dlabels #3.1 xpos 0.528 ypos 0.625 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex- > apo-overlay.2.cxs > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/PPEP3-apo- > peptide_overlay.2.png width 3110 height 2680 supersample 3 > 2dlabels #3.2 xpos 0.897 ypos 0.688 > color #2,4/:108-118 lightcyan ribb Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color lightcyan #2,4/:108-118 ribb Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color lightcyan #2,4/A:108-118 ribb Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color lightcyan #2,4/A:108-118 cartoon Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #2,4/A:108-118 lightcyan cartoons > 2dlabels #3.2 xpos 0.856 ypos 0.629 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex- > apo-overlay.2.cxs > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/PPEP3-apo- > peptide_overlay.2.png width 3110 height 2680 supersample 3 [Repeated 1 time(s)] > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex- > apo-overlay.2.cxs > select #4/A:111@NH2 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > hbonds sel reveal true 4 hydrogen bonds found > color #7 #fa2b31ff models > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PPE3-peptidecomplex- > apo-overlay.2.cxs ——— End of log from Mon Dec 30 17:49:48 2024 ——— opened ChimeraX session > show :161 atoms > label #4/A:161 text {0.one_letter_code}{0.number} height 25 > label #4/A:161 text {0.one_letter_code}{0.number} height fixed size 25 > transparency #2 0 atoms > color #2 #8b8b8b19 > color #2 #cdcdcd19 > color #2 #e2e2e219 > transparency #2 0 atoms > color sel byhetero > color #2 byhetat Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #2 byhetero > 2dlabels #3.2 xpos 0.879 ypos 0.409 > ~distance > hide #2 atoms, cartoons > show #2/A:161 atoms > show #2/A:161 atoms !@C,O Expected ',' or a keyword > show #2/A:161 atoms ~@C,O Expected ',' or a keyword > hide #2/A:161@C,O > 2dlabels #3.1 xpos 0.749 ypos 0.680 > hide #3.3 models > hide #3.4 models > 2dlabels #3.1 xpos 0.686 ypos 0.739 > show #4/A surfaces > color lightgrey surfaces > transparency 50 surfaces > show #4/A:131,133,104,127 atoms > 2dlabels #3.1 xpos 0.712 ypos 0.632 > select #4/E:3@CD2 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel HIS rotLib Dunbrack chain_A_E.pdb #4/E LEU 3: phi -113.1, psi 128.2 trans Changed 288 bond radii > swapaa interactive sel HIS rotLib Dunbrack chain_A_E.pdb #!4/E LEU 3: phi -113.1, psi 128.2 trans Changed 288 bond radii > swapaa #!4/E:3 HIS criteria 7 rotLib Dunbrack Using Dunbrack library chain_A_E.pdb #!4/E LEU 3: phi -113.1, psi 128.2 trans Applying HIS rotamer (chi angles: -63.7 94.6) to chain_A_E.pdb #!4/E HIS 3 > hide sel surfaces [Repeated 1 time(s)] > select 5591 atoms, 5731 bonds, 17 pseudobonds, 691 residues, 50 models selected > hide sel & #4.3.16#!2,4 surfaces > select #!4/E:3@NE2 1 atom, 1 residue, 1 model selected > select add #!4/A:161@CZ 2 atoms, 2 residues, 1 model selected > distance #!4/E:3@NE2 #!4/A:161@CZ Distance between chain_A_E.pdb #!4/E HIS 3 NE2 and /A TYR 161 CZ: 2.7Å > select #4/E:2@CA 1 atom, 1 residue, 1 model selected > select up 7 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel LEU rotLib Dunbrack chain_A_E.pdb #4/E PRO 2: phi -79.3, psi 110.5 trans Changed 45 bond radii > show #4/A surfaces > swapaa #!4/E:2 LEU criteria 2 rotLib Dunbrack Using Dunbrack library chain_A_E.pdb #!4/E PRO 2: phi -79.3, psi 110.5 trans Applying LEU rotamer (chi angles: -61.7 175.9) to chain_A_E.pdb #!4/E LEU 2 > select clear > lighting full > lighting shadows false > lighting simple > 2dlabels #3.1 xpos 0.668 ypos 0.587 > lighting full > lighting shadows false > lighting soft > lighting gentle > lighting full > lighting shadows false > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png > width 3110 height 2662 supersample 3 > lighting ambient 0.1 Expected keyword ""ambientColor"" or ""ambientIntensity"" > lighting ambientIntensity 0.1 > lighting ambientIntensity 0.3 > lighting ambientIntensity 0.4 > lighting ambientIntensity 0.5 > lighting full > lighting shadows false > lighting ambientColor black > lighting ambientColor lightgrey > 2dlabels #3.1 xpos 0.676 ypos 0.538 > lighting ambientColor lightgrey depthCue true > lighting soft > lighting soft multiShadow 512 > lighting soft multiShadow 1024 > lighting full > lighting shadows false > lighting gentlemultishadow 1024 Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a keyword > lighting gentle multiShadow 1024 > lighting softmultishadow 1024 Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a keyword > lighting full > lighting soft > lighting full > lighting soft > label #4/A > 104,131,133 text ""{0.one_letter_code}{number}"" size 25 height fix Unknown command: 104,131,133 text ""{0.one_letter_code}{number}"" size 25 height fix > ~label #4/A > 104,131,133 text ""{0.one_letter_code}{number}"" size 25 height fix Unknown command: 104,131,133 text ""{0.one_letter_code}{number}"" size 25 height fix > ~label #4/A:104,131,133,161 text ""{0.one_letter_code}{number}"" size 25 > height fix > label delete #4/A:104,131,133,161 text ""{0.one_letter_code}{number}"" size 25 > height fix Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label #4/A:104,131,133,161 text {0.one_letter_code}{number} size 25 height > fixed > ~label #4/A:104,131,133,161 text ""{0.one_letter_code}{0.number}"" size 25 > height fix > label delete #4/A:104,131,133,161 text ""{0.one_letter_code}{0.number}"" size > 25 height fix Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label #4/A:104,131,133,161 text {0.one_letter_code}{0.number} size 25 height > fixed > label #4/A:104,101,131,133,161 text {0.one_letter_code}{0.number} size 25 > height fixed > label #4/A:104,101,104,131,133,161 text {0.one_letter_code}{0.number} size > 25 height fixed > lighting full > lighting shadows false > hide #!6 models > select clear > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png > width 3110 height 2662 supersample 3 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select 5304 atoms, 5443 bonds, 18 pseudobonds, 655 residues, 16 models selected > ~select Nothing selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > ui tool show Contacts > contacts sel interModel false ignoreHiddenModels true select true > makePseudobonds false log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 7 contacts atom1 atom2 overlap distance chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CD2 0.076 3.564 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A GLY 127 O 0.027 3.273 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CG -0.083 3.573 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CE1 -0.167 3.807 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 NE2 -0.184 3.704 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 ND1 -0.194 3.714 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CB -0.392 4.152 7 contacts > contacts sel restrict cross interModel false ignoreHiddenModels true select > true makePseudobonds false log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 21 contacts atom1 atom2 overlap distance chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A HIS 153 NE2 0.294 2.986 chain_A_E.pdb #4/A HIS 157 CE1 chain_A_E.pdb #4/A ALA 200 CB 0.210 3.430 chain_A_E.pdb #4/A HIS 157 CE1 chain_A_E.pdb #4/A GLU 197 CD 0.048 3.592 chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A GLY 128 N 0.024 3.496 chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A ZN 701 ZN 0.016 2.224 chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A HIS 153 CD2 -0.020 3.420 chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A ALA 154 O -0.061 3.361 chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A GLY 128 CA -0.125 3.885 chain_A_E.pdb #4/A HIS 157 ND1 chain_A_E.pdb #4/A ALA 200 CB -0.151 3.671 chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A GLY 127 C -0.164 3.654 chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A ALA 200 CB -0.168 3.688 chain_A_E.pdb #4/A HIS 157 CD2 chain_A_E.pdb #4/A HIS 153 CD2 -0.185 3.705 chain_A_E.pdb #4/A GLY 127 O chain_A_E.pdb #4/E HIS 3 N -0.191 2.851 chain_A_E.pdb #4/A GLY 127 O chain_A_E.pdb #4/E HIS 3 CA -0.202 3.502 chain_A_E.pdb #4/A HIS 157 NE2 chain_A_E.pdb #4/A GLU 197 CD -0.242 3.762 chain_A_E.pdb #4/A HIS 157 CE1 chain_A_E.pdb #4/A GLU 197 OE2 -0.257 3.437 chain_A_E.pdb #4/A HIS 157 CB chain_A_E.pdb #4/A GLY 127 CA -0.324 4.084 chain_A_E.pdb #4/A HIS 157 CE1 chain_A_E.pdb #4/A GLU 197 OE1 -0.332 3.512 chain_A_E.pdb #4/A GLY 127 O chain_A_E.pdb #4/E GLU 1 O -0.345 3.185 chain_A_E.pdb #4/A HIS 157 CD2 chain_A_E.pdb #4/A HIS 153 O -0.360 3.540 chain_A_E.pdb #4/A HIS 157 CD2 chain_A_E.pdb #4/A HIS 153 NE2 -0.365 3.765 21 contacts > ~select Nothing selected > contacts sel restrict #4/A interModel false ignoreHiddenModels true select > true makePseudobonds false log true No atoms match given atom specifier > contacts sel interModel false ignoreHiddenModels true select true > makePseudobonds false log true No atoms match given atom specifier > select up 2 atoms, 1 bond, 1 residue, 1 model selected > contacts sel restrict #4/A interModel false ignoreHiddenModels true select > true makePseudobonds false log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 1 contacts atom1 atom2 overlap distance chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/A GLY 128 CA 0.153 3.367 1 contacts > contacts sel restrict #4/A:161 interModel false ignoreHiddenModels true > select true makePseudobonds false log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 0 contacts atom1 atom2 overlap distance No contacts > ~select Nothing selected > select #4/E:2 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/E:3 10 atoms, 10 bonds, 1 residue, 1 model selected > contacts sel interModel false ignoreHiddenModels true select true > makePseudobonds false log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 35 contacts atom1 atom2 overlap distance chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CB 0.698 2.942 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CE2 0.623 2.897 chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CZ 0.547 2.703 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CZ 0.405 2.965 chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CE2 0.335 3.065 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CD2 0.166 3.354 chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/A GLY 128 CA 0.153 3.367 chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 OH 0.085 2.615 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CD2 0.076 3.564 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CE1 0.074 3.446 chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CE1 0.044 3.356 chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/E GLU 1 CB 0.031 3.489 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A GLY 127 O 0.027 3.273 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CG 0.008 3.632 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CG -0.083 3.573 chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/E GLU 1 O -0.118 2.778 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 O -0.122 3.302 chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/E GLU 1 CB -0.141 3.661 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CA -0.152 3.792 chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/E GLU 1 CG -0.152 3.672 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CE1 -0.167 3.807 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 NE2 -0.184 3.704 chain_A_E.pdb #4/E HIS 3 N chain_A_E.pdb #4/A GLY 127 O -0.191 2.851 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 ND1 -0.194 3.714 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 OH -0.199 3.419 chain_A_E.pdb #4/E HIS 3 CA chain_A_E.pdb #4/A GLY 127 O -0.202 3.502 chain_A_E.pdb #4/E HIS 3 ND1 chain_A_E.pdb #4/E GLU 1 C -0.223 3.473 chain_A_E.pdb #4/E HIS 3 CD2 chain_A_E.pdb #4/A ARG 111 NH2 -0.275 3.675 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CD1 -0.310 3.830 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 C -0.317 3.687 chain_A_E.pdb #4/E HIS 3 CD2 chain_A_E.pdb #4/A TYR 161 OH -0.336 3.556 chain_A_E.pdb #4/E HIS 3 O chain_A_E.pdb #4/A ILE 126 CA -0.339 3.639 chain_A_E.pdb #4/E HIS 3 CB chain_A_E.pdb #4/A HIS 157 CB -0.392 4.152 chain_A_E.pdb #4/E HIS 3 O chain_A_E.pdb #4/A ILE 126 CG1 -0.392 3.692 chain_A_E.pdb #4/E HIS 3 C chain_A_E.pdb #4/A TRP 120 CH2 -0.397 3.767 35 contacts > select #4/E:2 8 atoms, 7 bonds, 1 residue, 1 model selected > contacts sel interModel false ignoreHiddenModels true select true > makePseudobonds false log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 13 contacts atom1 atom2 overlap distance chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899 chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A HIS 104 NE2 0.479 3.041 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A HIS 104 CE1 0.187 3.453 chain_A_E.pdb #4/E LEU 2 CB chain_A_E.pdb #4/A ILE 126 CD1 0.175 3.585 chain_A_E.pdb #4/E LEU 2 CG chain_A_E.pdb #4/A ILE 126 CD1 -0.028 3.788 chain_A_E.pdb #4/E LEU 2 CG chain_A_E.pdb #4/A LEU 105 CD1 -0.039 3.799 chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A LEU 105 CD1 -0.134 3.894 chain_A_E.pdb #4/E LEU 2 CA chain_A_E.pdb #4/A ILE 126 CD1 -0.142 3.902 chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CG1 -0.170 3.930 chain_A_E.pdb #4/E LEU 2 CB chain_A_E.pdb #4/A LEU 105 CD1 -0.289 4.049 13 contacts > show #4/A:105 atoms > select clear > 2dlabels #3.1 xpos 0.679 ypos 0.495 > label #4/A:104,101,104,105,131,133,161 text {0.one_letter_code}{0.number} > size 25 height fixed > 2dlabels #3.1 xpos 0.637 ypos 0.492 > 2dlabels #3.1 xpos 0.682 ypos 0.492 > ui tool show Clashes > clashes overlapCutoff 0.4 interModel false intraRes true ignoreHiddenModels > true log true Allowed overlap: 0.4 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 20 clashes atom1 atom2 overlap distance chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899 chain_A_E.pdb #4/A ILE 126 CD1 chain_A_E.pdb #4/E LEU 2 CD2 0.825 2.935 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CB 0.698 2.942 chain_A_E.pdb #4/A TYR 161 CE2 chain_A_E.pdb #4/E HIS 3 CE1 0.623 2.897 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A LEU 176 CD2 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ARG 222 CB 0.586 3.174 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A GLU 154 OE2 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A PGE 702 C3 0.555 2.745 chain_A_E.pdb #4/A TYR 161 CZ chain_A_E.pdb #4/E HIS 3 NE2 0.547 2.703 chain_A_E.pdb #4/A GLU 63 O chain_A_E.pdb #4/A GLU 66 CG 0.542 2.758 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A VAL 30 CG1 (alt loc A) PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A VAL 54 CG2 0.499 3.261 chain_A_E.pdb #4/A PHE 190 CE2 chain_A_E.pdb #4/A GLU 197 CD 0.499 3.141 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A GLU 179 CD PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A ARG 222 NH1 0.493 3.027 chain_A_E.pdb #4/A HIS 104 NE2 chain_A_E.pdb #4/E LEU 2 CD1 0.479 3.041 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A GLU 154 OE1 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A BCN 704 O21 0.473 2.367 chain_A_E.pdb #4/A VAL 123 CG1 chain_A_E.pdb #4/E PRO 5 CD 0.457 3.303 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A THR 93 O PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A PEG 703 C1 0.443 2.857 chain_A_E.pdb #4/A PHE 190 CE2 chain_A_E.pdb #4/A GLU 197 CG 0.427 3.213 PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A THR 93 CB PPEPgeo-4-3-XDSnewest_ESRF20230721_refine_039.pdb #2/A PEG 703 C2 0.422 3.338 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CZ 0.405 2.965 20 clashes > clashes overlapCutoff 0.4 interModel false intraRes true intraModel false > ignoreHiddenModels true log true Allowed overlap: 0.4 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > select #4/E:2 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show Clashes > clashes overlapCutoff 0.4 interModel false intraRes true intraModel false > ignoreHiddenModels true log true Allowed overlap: 0.4 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > select #4/E:3 10 atoms, 10 bonds, 1 residue, 1 model selected > clashes overlapCutoff 0.4 interModel false intraRes true intraModel false > ignoreHiddenModels true log true Allowed overlap: 0.4 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > select clear > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.cxs > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png > width 3110 height 2662 supersample 3 > show #4/A:126 atoms > label #4/A:104,101,104,105,131,133,161,126 text > {0.one_letter_code}{0.number} size 25 height fixed > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png > width 3110 height 2662 supersample 3 > 2dlabels #3.2 xpos 0.820 ypos 0.383 > 2dlabels #3.2 xpos 0.848 ypos 0.197 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.png > width 3110 height 2662 supersample 3 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.cxs > select #4/E3 Nothing selected > select #4/E:3 10 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack chain_A_E.pdb #4/E HIS 3: phi -113.1, psi 128.2 trans Changed 600 bond radii > swapaa interactive sel ARG rotLib Dunbrack chain_A_E.pdb #!4/E HIS 3: phi -113.1, psi 128.2 trans Changed 600 bond radii > swapaa #!4/E:3 ARG criteria 10 rotLib Dunbrack Using Dunbrack library chain_A_E.pdb #!4/E HIS 3: phi -113.1, psi 128.2 trans Applying ARG rotamer (chi angles: -176.0 -179.9 -63.3 -84.3) to chain_A_E.pdb #!4/E ARG 3 > contacts sel interModel false ignoreHiddenModels true select true > makePseudobonds false log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 5 contacts atom1 atom2 overlap distance chain_A_E.pdb #!4/E ARG 3 N chain_A_E.pdb #!4/A GLY 127 O -0.191 2.851 chain_A_E.pdb #!4/E ARG 3 CA chain_A_E.pdb #!4/A GLY 127 O -0.202 3.502 chain_A_E.pdb #!4/E ARG 3 O chain_A_E.pdb #!4/A ILE 126 CA -0.339 3.639 chain_A_E.pdb #!4/E ARG 3 O chain_A_E.pdb #!4/A ILE 126 CG1 -0.392 3.692 chain_A_E.pdb #!4/E ARG 3 C chain_A_E.pdb #!4/A TRP 120 CH2 -0.397 3.767 5 contacts > contacts sel interModel false ignoreHiddenModels true select true > makePseudobonds false log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 14 contacts atom1 atom2 overlap distance chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E PRO 4 CB 0.103 3.537 chain_A_E.pdb #!4/A GLY 127 O chain_A_E.pdb #!4/E ARG 3 CB 0.027 3.273 chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E PRO 4 CA -0.136 3.776 chain_A_E.pdb #!4/A ILE 126 CG1 chain_A_E.pdb #!4/A TRP 120 CZ3 -0.147 3.787 chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E PRO 4 CD -0.158 3.798 chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E PRO 4 N -0.168 3.568 chain_A_E.pdb #!4/A ILE 126 CG1 chain_A_E.pdb #!4/E LEU 2 CD2 -0.170 3.930 chain_A_E.pdb #!4/A GLY 127 O chain_A_E.pdb #!4/E ARG 3 N -0.191 2.851 chain_A_E.pdb #!4/A GLY 127 O chain_A_E.pdb #!4/E ARG 3 CA -0.202 3.502 chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/A ILE 126 CD1 -0.246 3.886 chain_A_E.pdb #!4/A ILE 126 CA chain_A_E.pdb #!4/E ARG 3 O -0.339 3.639 chain_A_E.pdb #!4/A GLY 127 O chain_A_E.pdb #!4/E GLU 1 O -0.345 3.185 chain_A_E.pdb #!4/E ARG 3 O chain_A_E.pdb #!4/A ILE 126 CG1 -0.392 3.692 chain_A_E.pdb #!4/A TRP 120 CH2 chain_A_E.pdb #!4/E ARG 3 C -0.397 3.767 14 contacts > swapaa #!4/E:3 ARG criteria 14 rotLib Dunbrack Using Dunbrack library chain_A_E.pdb #!4/E ARG 3: phi -113.1, psi 128.2 trans Applying ARG rotamer (chi angles: -59.7 -73.4 -178.2 -179.3) to chain_A_E.pdb #!4/E ARG 3 > select #4/E:3 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Clashes > clashes overlapCutoff 0.4 interModel false intraRes true intraModel false > ignoreHiddenModels true log true Allowed overlap: 0.4 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > clashes sel overlapCutoff 0.4 interModel false intraRes true intraModel > false ignoreHiddenModels true log true Allowed overlap: 0.4 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > clashes sel overlapCutoff 0.10000000000000003 interModel false intraRes true > intraModel false ignoreHiddenModels true log true Allowed overlap: 0.1 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > clashes sel restrict cross overlapCutoff 0.10000000000000003 interModel > false intraRes true intraModel false ignoreHiddenModels true log true Allowed overlap: 0.1 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > clashes sel restrict cross overlapCutoff 0.7 interModel false intraRes true > intraModel false ignoreHiddenModels true log true Allowed overlap: 0.7 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > 2dlabels #3.1 xpos 0.672 ypos 0.491 > 2dlabels #3.2 xpos 0.829 ypos 0.444 > select clear > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg.png > width 1555 height 1331 supersample 3 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.arg.cxs > select #4/E:3 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Contacts > contacts sel interModel false ignoreHiddenModels true select true > makePseudobonds false log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 37 contacts atom1 atom2 overlap distance chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/E GLU 1 OE1 0.891 1.769 chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/E GLU 1 CD 0.604 2.916 chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A ARG 111 NE 0.562 2.718 chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A ARG 111 NH2 0.454 2.826 chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/A TYR 161 OH 0.359 2.341 chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/A TYR 161 OH 0.322 2.748 chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/E GLU 1 OE1 0.321 2.709 chain_A_E.pdb #4/E ARG 3 CD chain_A_E.pdb #4/A ARG 111 NH2 0.171 3.349 chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A ARG 111 CZ 0.099 3.151 chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 CD2 0.092 3.548 chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A GLU 196 OE2 0.058 2.602 chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/E GLU 1 CG 0.048 3.472 chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A GLY 127 O 0.028 3.272 chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A GLU 196 CD -0.012 3.532 chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/E GLU 1 CG -0.022 3.542 chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 CG -0.073 3.563 chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/E GLU 1 CD -0.074 3.564 chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/A TYR 161 CZ -0.096 3.346 chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/A TYR 161 CZ -0.116 3.366 chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 CE1 -0.157 3.797 chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 NE2 -0.167 3.687 chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/A TYR 161 OH -0.168 2.868 chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 ND1 -0.187 3.707 chain_A_E.pdb #4/E ARG 3 N chain_A_E.pdb #4/A GLY 127 O -0.191 2.851 chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/E GLU 1 CG -0.192 3.682 chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/E GLU 1 CB -0.194 3.714 chain_A_E.pdb #4/E ARG 3 CA chain_A_E.pdb #4/A GLY 127 O -0.202 3.502 chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/A TYR 161 CE2 -0.212 3.612 chain_A_E.pdb #4/E ARG 3 CZ chain_A_E.pdb #4/A GLU 196 OE2 -0.302 3.332 chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/E GLU 1 CD -0.309 3.829 chain_A_E.pdb #4/E ARG 3 CG chain_A_E.pdb #4/E GLU 1 O -0.320 3.620 chain_A_E.pdb #4/E ARG 3 O chain_A_E.pdb #4/A ILE 126 CA -0.339 3.639 chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/A GLU 196 CG -0.344 3.864 chain_A_E.pdb #4/E ARG 3 NE chain_A_E.pdb #4/A TYR 161 CE2 -0.363 3.763 chain_A_E.pdb #4/E ARG 3 CB chain_A_E.pdb #4/A HIS 157 CB -0.386 4.146 chain_A_E.pdb #4/E ARG 3 O chain_A_E.pdb #4/A ILE 126 CG1 -0.392 3.692 chain_A_E.pdb #4/E ARG 3 C chain_A_E.pdb #4/A TRP 120 CH2 -0.397 3.767 37 contacts > ui tool show Clashes > clashes sel restrict cross overlapCutoff 0.7 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.7 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > clashes sel restrict cross overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 3 clashes atom1 atom2 overlap distance chain_A_E.pdb #4/E ARG 3 NH2 chain_A_E.pdb #4/E GLU 1 OE1 0.891 1.769 chain_A_E.pdb #4/E GLU 1 CD chain_A_E.pdb #4/E ARG 3 NH2 0.604 2.916 chain_A_E.pdb #4/A ARG 111 NE chain_A_E.pdb #4/E ARG 3 NH1 0.562 2.718 3 clashes > select clear > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg.clashes.png > width 3110 height 2662 supersample 3 > ui tool show Rotamers > select #4/E:3 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel HIS rotLib Dunbrack chain_A_E.pdb #4/E ARG 3: phi -113.1, psi 128.2 trans Changed 288 bond radii > swapaa #!4/E:3 HIS criteria 7 rotLib Dunbrack Using Dunbrack library chain_A_E.pdb #!4/E ARG 3: phi -113.1, psi 128.2 trans Applying HIS rotamer (chi angles: -63.7 94.6) to chain_A_E.pdb #!4/E HIS 3 > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > select #4/E:3 10 atoms, 10 bonds, 1 residue, 1 model selected > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 3 clashes atom1 atom2 overlap distance chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CB 0.642 2.998 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CE2 0.614 2.906 chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CZ 0.560 2.690 3 clashes > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 3 clashes atom1 atom2 overlap distance chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/E GLU 1 CB 0.642 2.998 chain_A_E.pdb #4/E HIS 3 CE1 chain_A_E.pdb #4/A TYR 161 CE2 0.614 2.906 chain_A_E.pdb #4/E HIS 3 NE2 chain_A_E.pdb #4/A TYR 161 CZ 0.560 2.690 3 clashes > 2dlabels #3.1 xpos 0.650 ypos 0.501 > 2dlabels #3.1 xpos 0.736 ypos 0.575 > select clear > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.His.clashes.png > width 3110 height 2662 supersample 3 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 0 clashes atom1 atom2 overlap distance No clashes > select #4/E:2 8 atoms, 7 bonds, 1 residue, 1 model selected > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 4 clashes atom1 atom2 overlap distance chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899 chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191 4 clashes > select clear > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Leu.clashes.png > width 1555 height 1331 supersample 3 > select #4/E:3 10 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack chain_A_E.pdb #4/E HIS 3: phi -113.1, psi 128.2 trans Changed 600 bond radii > swapaa #!4/E:3 ARG criteria 46 rotLib Dunbrack Using Dunbrack library chain_A_E.pdb #!4/E HIS 3: phi -113.1, psi 128.2 trans Applying ARG rotamer (chi angles: -62.1 -78.1 73.6 81.6) to chain_A_E.pdb #!4/E ARG 3 > select add #4/E:2 12 atoms, 10 bonds, 2 residues, 1 model selected > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 4 clashes atom1 atom2 overlap distance chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899 chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191 4 clashes > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true radius 0.1 log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 4 clashes atom1 atom2 overlap distance chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899 chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191 4 clashes > select add #4/E:3 19 atoms, 17 bonds, 2 residues, 1 model selected > clashes sel overlapCutoff 0.5 interModel false intraRes true > ignoreHiddenModels true radius 0.1 log true Allowed overlap: 0.5 H-bond overlap reduction: 0.4 Ignore clashes between atoms separated by 4 bonds or less Detect intra-residue clashes: True Detect intra-molecule clashes: True 7 clashes atom1 atom2 overlap distance chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/E GLU 1 CG 1.608 1.912 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD2 0.881 2.879 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CD1 0.861 2.899 chain_A_E.pdb #4/E LEU 2 CD2 chain_A_E.pdb #4/A ILE 126 CD1 0.825 2.935 chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/E GLU 1 CD 0.774 2.746 chain_A_E.pdb #4/E ARG 3 NH1 chain_A_E.pdb #4/E GLU 1 CB 0.752 2.768 chain_A_E.pdb #4/E LEU 2 CD1 chain_A_E.pdb #4/A LEU 105 CG 0.569 3.191 7 clashes > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.arg_leu.cxs > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png > width 3110 height 2662 supersample 3 > select clear > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png > width 3110 height 2662 supersample 3 > 2dlabels #3.1 xpos 0.733 ypos 0.599 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png > width 3110 height 2662 supersample 3 > lighting soft > lighting full > lighting shadows false > lighting direction -1 -1 1 Invalid ""direction"" argument: Need exactly 3 ','-separated 3-tuple of numbers > lighting direction -1, -1, 1, Invalid ""direction"" argument: Expected a number > lighting direction -1, -1, 1 > lighting direction -1, -1, -1 > lighting simple [Repeated 1 time(s)] > lighting soft > lighting full > lighting shadows false > lighting direction 0.577,-0.577,-0.5771 > lighting full > lighting shadows false > lighting ambie 1.55771 Expected keyword ""ambientColor"" or ""ambientIntensity"" > lighting ambientIntensity 1.55771 > lighting ambientIntensity 0.3 > lighting ambientIntensity 0.5 > lighting ambientIntensity 0.6 > lighting ambientIntensity 0.75 > lighting ambientIntensity 0.75 multiShadow 124 > lighting ambientIntensity 0.75 multiShadow 1024 > lighting ambientIntensity 0.75 multiShadow 256 > 2dlabels #3.2 xpos 0.810 ypos 0.315 > 2dlabels #3.2 xpos 0.805 ypos 0.232 > label #4/A:104,101,104,105,131,133,161,126,157 text > {0.one_letter_code}{0.number} size 25 height fixed > label #4/A:104,101,104,105,131,133,161,126,157,111 text > {0.one_letter_code}{0.number} size 25 height fixed > 2dlabels #3.2 xpos 0.766 ypos 0.187 > 2dlabels #3.2 xpos 0.803 ypos 0.157 > label #4/A:104,101,104,105,131,133,161,126,157,111,113 text > {0.one_letter_code}{0.number} size 25 height fixed > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png > width 3110 height 2662 supersample 3 > 2dlabels #3.1 xpos 0.665 ypos 0.596 > 2dlabels #3.1 xpos 0.687 ypos 0.572 > 2dlabels #3.2 xpos 0.783 ypos 0.170 > 2dlabels #3.2 xpos 0.837 ypos 0.173 > 2dlabels #3.1 xpos 0.631 ypos 0.584 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png > width 3110 height 2662 supersample 3 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.arg_leu.cxs > 2dlabels #3.2 xpos 0.797 ypos 0.172 > 2dlabels #3.1 xpos 0.598 ypos 0.585 > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3-modelling.arg_leu.cxs > save > /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/PNG/P3-P2-modelled.Arg_Leu.clashes.png > width 3110 height 2662 supersample 3 > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/P2-P3.ar_leu.x3d Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 127, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 138, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 62, in display run(session, cmd) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 101, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core_formats/__init__.py"", line 120, in save return save_x3d(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 1205, in save_x3d m.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1393, in x3d_needs d.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/label/label2d.py"", line 724, in x3d_needs from .. import x3d ImportError: cannot import name 'x3d' from 'chimerax' (unknown location) ImportError: cannot import name 'x3d' from 'chimerax' (unknown location) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/label/label2d.py"", line 724, in x3d_needs from .. import x3d See log for complete Python traceback. > save /Users/ubaumann/Documents/Papers/PPEP-3-_NEW/Figures/test-p3p2.x3d Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 127, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 138, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 62, in display run(session, cmd) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 101, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core_formats/__init__.py"", line 120, in save return save_x3d(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/session.py"", line 1205, in save_x3d m.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1393, in x3d_needs d.x3d_needs(x3d_scene) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/label/label2d.py"", line 724, in x3d_needs from .. import x3d ImportError: cannot import name 'x3d' from 'chimerax' (unknown location) ImportError: cannot import name 'x3d' from 'chimerax' (unknown location) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/label/label2d.py"", line 724, in x3d_needs from .. import x3d See log for complete Python traceback. OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGQ3D/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 11881.61.3 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7.2 (23H311) Kernel Version: Darwin 23.6.0 Time since boot: 21 days, 7 hours, 15 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: ASUS CG32U: Resolution: 6720 x 3780 UI Looks like: 3360 x 1890 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.23.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal 1.10 Input/Output fixed Eric Pettersen Tom Goddard all ChimeraX